Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 71.48 kDa 
• Atom Count: 5055 
• Residue Count: 587 
• Unique protein chains: 3

1WQV

Human Factor Viia-Tissue Factor Complexed with propylsulfonamide-D-Thr-Met-p-aminobenzamidine

• DOI: 10.2210/pdb1WQV/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Homo sapiens, Escherichia coli
• Mutation(s): No 


• Deposited: 2004-10-02 Released: 2005-10-02 
• Deposition Author(s): Kadono, S., Sakamoto, A., Kikuchi, Y., Oh-eda, M., Yabuta, N., Koga, T., Hattori, K., Shiraishi, T., Haramura, M., Kodama, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.272 
• R-Value Work: 0.218 

Literature

Crystal structure of human factor VIIa/tissue factor in complex with peptide mimetic inhibitor

Kadono, S., Sakamoto, A., Kikuchi, Y., Oh-eda, M., Yabuta, N., Koga, T., Hattori, K., Shiraishi, T., Haramura, M., Kodama, H., Esaki, T., Sato, H., Watanabe, Y., Itoh, S., Ohta, M., Kozono, T.

(2004) Biochem Biophys Res Commun 324: 1227-1233

• PubMed: 15504346 
• DOI: 10.1016/j.bbrc.2004.09.182
• Primary Citation of Related Structures:  
  1WQV


• PubMed Abstract: 
  

The 3D structure of human factor VIIa/soluble tissue factor in complex with a peptide mimetic inhibitor, propylsulfonamide-D-Thr-Met-p-aminobenzamidine, is determined by X-ray crystallography. As compared with the interactions between thrombin and thrombin inhibitors, the interactions at S2 and S3 sites characteristic of factor VIIa and factor VIIa inhibitors are revealed. The S2 site has a small pocket, which is filled by the hydrophobic methionine side chain in P2. The small S3 site fits the small size residue, D-threonine in P3. The structural data and SAR data of the peptide mimetic inhibitor show that these interactions in the S2 and S3 sites play an important role for the improvement of selectivity versus thrombin. The results will provide valuable information for the structure-based drug design of specific inhibitors for FVIIa/TF.

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Organizational Affiliation: 

Fuji Gotemba Research Labs, Chugai Pharmaceutical Co., Ltd., 1-135 Komakado, Gotemba, Shizuoka 412-8513, Japan. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VII	L	152	Homo sapiens	Mutation(s): 0  Gene Names: F7 EC: 3.4.21.21
Find proteins for P08709 (Homo sapiens) Explore P08709  Go to UniProtKB:  P08709
NIH Common Fund Data Resources
PHAROS:  P08709 GTEx:  ENSG00000057593

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Coagulation factor VII	H	254	Homo sapiens	Mutation(s): 0  Gene Names: F7 EC: 3.4.21.21
Find proteins for P08709 (Homo sapiens) Explore P08709  Go to UniProtKB:  P08709
NIH Common Fund Data Resources
PHAROS:  P08709 GTEx:  ENSG00000057593

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Tissue factor	T	218	Homo sapiens	Mutation(s): 0  Gene Names: F3
Find proteins for P13726 (Homo sapiens) Explore P13726  Go to UniProtKB:  P13726
NIH Common Fund Data Resources
PHAROS:  P13726 GTEx:  ENSG00000117525

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PSM	H	N-[DIHYDROXY(PROPYL)-LAMBDA~4~-SULFANYL]THREONYL-N~1~-{4-[AMINO(IMINO)METHYL]BENZYL}METHIONINAMIDE C20 H33 N5 O5 S2 AIIJKVORRBMJHS-RRQGHBQHSA-N
BGC	L	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
FUC	L	alpha-L-fucopyranose C6 H12 O5 SHZGCJCMOBCMKK-SXUWKVJYSA-N
CA	H, L	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CGU	L	L-PEPTIDE LINKING	C6 H9 N O6		GLU

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
PSM	IC50:  130   nM  Binding MOAD
PSM	IC50 :  130   nM  PDBBind

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 0.272 
• R-Value Work: 0.218 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.39	α = 90
b = 82.42	β = 90
c = 123.51	γ = 90

Software Package:

Software Name	Purpose
CNX	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-10-02 
• Released Date: 2005-10-02 
Deposition Author(s): Kadono, S., Sakamoto, A., Kikuchi, Y., Oh-eda, M., Yabuta, N., Koga, T., Hattori, K., Shiraishi, T., Haramura, M., Kodama, H.

Revision History 

• Version 1.0: 2005-10-02
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary